From: Atila Petrosian (atila.petrosian_at_gmail.com)
Date: Fri Oct 30 2015 - 07:46:10 CDT

I could see prmtop and mdcrd files using vmd without any problem.

I there was a problem with the topology file, I could not see prmtop and
mdcrd files.

Is this problem related to VMD?

On Fri, Oct 30, 2015 at 3:51 PM, Diego Vazquez <dsvazquez86_at_gmail.com>
wrote:

> If your trajectory is in .nc there should be no problem with that, vmd
> recognize automatically the binary file...unless you have a problem with
> the topology file (e.g. the atom number don´t match!!)
> On Oct 30, 2015 8:17 AM, "Atila Petrosian" <atila.petrosian_at_gmail.com>
> wrote:
>
>> Dear Diego,
>>
>> Thanks for your answer.
>>
>> I converted .mdcrd file to .nc file. In VMD, there is amber7 parm in file
>> type section of molecule file browser window. But there is no netcdf in
>> file type section.
>>
>> After loading .prmtop as AMBER7 parm, how to load .nc file as netcdf? I
>> load .nc file, but nothing happened.
>>
>> I have a general question. Is there all things needed for analysis of
>> trajectory in .nc file?
>>
>> After converting .mdcrd files to .nc files, can I deleted .mdcrd files?
>> There is no enough memory in my computer system.
>>
>> Best,
>> Atila
>>
>> On Fri, Oct 30, 2015 at 12:32 PM, Diego Vazquez <dsvazquez86_at_gmail.com>
>> wrote:
>>
>>> Dear Atila,
>>>
>>> Just load your .prmtop as AMBER7 parm and the .nc file into the prmtop
>>> as NetCDF...that's all!
>>>
>>> On 30 October 2015 at 04:22, Atila Petrosian <atila.petrosian_at_gmail.com>
>>> wrote:
>>>
>>>> Dear vmd users,
>>>>
>>>> I saw my amber trajectories by loading *.prmtop and *.mdcrd fils.
>>>>
>>>> Now, I have *.netcdf file instead of *.mdcrd file.
>>>>
>>>> In this case, how to see my new trajectory using vmd?
>>>>
>>>> Best,
>>>> Atila
>>>>
>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> **************************************************
>>> Lic. Diego Sebastian Vazquez
>>> Laboratorio de Biofísica de Proteínas
>>> IQUIFIB - Departamento de Química Biológica
>>> Facultad de Farmacia y Bioquímica
>>> Universidad de Buenos Aires, Argentina
>>> Junín 956 (1113)
>>> Tel: 1534476306
>>> dsv_at_qb.ffyb.uba.ar
>>>
>>
>>